Former Enron boss Jeffrey Skilling has been charged with 35 counts of fraud, insider trading and lying about the state of the firm's finances.
SKilling's arrest follows a guilty plea by a colleague in January
The charges come after Mr Skilling surrendered himself to the FBI at its Houston headquarters.
With bail set at $5m, the 50-year-old - the highest ranking Enron executive at the company yet to be indicted - denied all the charges.
Investigations now turn towards former Enron chairman Ken Lay.
Mr Lay currently remains a free man, and like Mr Skilling has professed his innocence.
Speaking for Mr Skilling, attorney Dan Petrocelli told reporters that his client was being made a scapegoat.
"He didn't steal, he didn't lie, he didn't take anyone's money," he said outside court.
"In the 60 pages of charges filed by the US government, they don't even accuse him of these things, and it's not for lack of trying."
Richard Causey was briefly handcuffed after surrendering
The indictment, however, reads rather differently, as US Deputy Attorney General James Comey told a Washington DC news conference.
Mr Sklling and his associates, he said, conspired "to cook the books to create the illusion that (Enron) was a growing, robust company with limitless potential".
In fact - and in contrast - it was "an increasingly troubled business kept afloat by a lifeline of gimmicks and maneouvres".
The indictment says Mr Skilling made $89m by selling shares at "artificially inflated prices".
As well as the charges against Mr Skilling, several fresh accusations are levelled at former Chief Accounting Officer Richard Causey, indicted a month ago.
The former chief executive's surrender to the FBI comes a month after former Enron chief financial officer Andrew Fastow pleaded guilty to two fraud counts in exchange for a 10-year prison sentence.
It is believed that Mr Fastow and his wife Lea - who also worked for Enron - cut a deal with prosecutors to reveal what they know about others' involvement in the fraud.
Andrew Fastow is thought to have cut a deal
Both Mr Fastow and his wife are now free on bail until formal sentencing in April.
Enron collapsed and filed for bankruptcy in December 2001, after it was revealed that though false accounting it had hidden billions of dollars in debt.
The episode has rocked corporate America.
Harvard-educated Mr Skilling joined Enron in 1990 and was quickly promoted.
In 1997 he became president and chief operating officer, before in February 2001 becoming chief executive.
Mr Skilling was a key driver in Enron's transformation from a sleepy pipeline company into a corporate giant and darling of Wall Street.
But in August 2001 - after just six months at the top of the company - he unexpectedly resigned, saying he wanted time to enjoy life.
According to published records, he pocketed $15m in stock options, and in testimony two years ago to the US House Energy and Commerce Committee said: "I absolutely, unequivocally thought the company was in good shape."
This however was questioned by former Enron employee Sherron Watkins, the main whistleblower at the company.
In her own testimony to Congress she laid the blame firmly at the feet of Mr Skilling and Mr Fastow, while clearing Mr Lay.
Ben Glisan, a former treasurer at Enron is so far the only executive from the company to be jailed.
He was given a five year sentence back in September.